[{"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevFluids.3.103303","department":[{"_id":"BjHo"}],"has_accepted_license":"1","ec_funded":1,"acknowledgement":"This work was partially supported by the Israel Science Foundation (ISF; Grant No. 882/15) and the Binational USA-Israel Foundation (BSF; Grant No. 2016145).","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"16","date_updated":"2023-09-13T08:57:05Z","type":"journal_article","oa_version":"Submitted Version","scopus_import":"1","date_published":"2018-10-16T00:00:00Z","external_id":{"isi":["000447469200001"]},"file":[{"file_id":"5043","date_updated":"2020-07-14T12:45:04Z","access_level":"open_access","checksum":"7fc0a2322214d1c04debef36d5bf2e8a","file_name":"IST-2018-1062-v1+1_PhysRevFluids.3.103303.pdf","date_created":"2018-12-12T10:13:56Z","relation":"main_file","content_type":"application/pdf","creator":"system","file_size":1838431}],"oa":1,"ddc":["532"],"_id":"16","title":"Mixing layer instability and vorticity amplification in a creeping viscoelastic flow","publication":"Physical Review Fluids","publication_status":"published","abstract":[{"text":"We report quantitative evidence of mixing-layer elastic instability in a viscoelastic fluid flow between two widely spaced obstacles hindering a channel flow at Re 1 and Wi 1. Two mixing layers with nonuniform shear velocity profiles are formed in the region between the obstacles. The mixing-layer instability arises in the vicinity of an inflection point on the shear velocity profile with a steep variation in the elastic stress. The instability results in an intermittent appearance of small vortices in the mixing layers and an amplification of spatiotemporal averaged vorticity in the elastic turbulence regime. The latter is characterized through scaling of friction factor with Wi and both pressure and velocity spectra. Furthermore, the observations reported provide improved understanding of the stability of the mixing layer in a viscoelastic fluid at large elasticity, i.e., Wi 1 and Re 1 and oppose the current view of suppression of vorticity solely by polymer additives.","lang":"eng"}],"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"author":[{"first_name":"Atul","last_name":"Varshney","full_name":"Varshney, Atul","orcid":"0000-0002-3072-5999","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Steinberg, Victor","first_name":"Victor","last_name":"Steinberg"}],"quality_controlled":"1","citation":{"ama":"Varshney A, Steinberg V. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. <i>Physical Review Fluids</i>. 2018;3(10). doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.3.103303\">10.1103/PhysRevFluids.3.103303</a>","ieee":"A. Varshney and V. Steinberg, “Mixing layer instability and vorticity amplification in a creeping viscoelastic flow,” <i>Physical Review Fluids</i>, vol. 3, no. 10. American Physical Society, 2018.","short":"A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).","chicago":"Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity Amplification in a Creeping Viscoelastic Flow.” <i>Physical Review Fluids</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevFluids.3.103303\">https://doi.org/10.1103/PhysRevFluids.3.103303</a>.","ista":"Varshney A, Steinberg V. 2018. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. 3(10), 103303.","apa":"Varshney, A., &#38; Steinberg, V. (2018). Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. <i>Physical Review Fluids</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevFluids.3.103303\">https://doi.org/10.1103/PhysRevFluids.3.103303</a>","mla":"Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity Amplification in a Creeping Viscoelastic Flow.” <i>Physical Review Fluids</i>, vol. 3, no. 10, 103303, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.3.103303\">10.1103/PhysRevFluids.3.103303</a>."},"year":"2018","publist_id":"8039","isi":1,"intvolume":"         3","article_number":"103303","status":"public","date_created":"2018-12-11T11:44:10Z","month":"10","issue":"10","volume":3,"pubrep_id":"1062","article_type":"original","publisher":"American Physical Society","file_date_updated":"2020-07-14T12:45:04Z"},{"file":[{"creator":"dernst","content_type":"application/pdf","file_size":1603844,"relation":"main_file","date_created":"2018-12-17T12:52:12Z","file_name":"2018_LNCS_Kragl.pdf","checksum":"c64fff560fe5a7532ec10626ad1c215e","access_level":"open_access","date_updated":"2020-07-14T12:45:04Z","file_id":"5705"}],"external_id":{"isi":["000491481600005"]},"date_published":"2018-07-18T00:00:00Z","page":"79 - 102","alternative_title":["LNCS"],"scopus_import":"1","oa_version":"Published Version","date_updated":"2023-09-13T08:45:09Z","type":"conference","day":"18","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","department":[{"_id":"ToHe"}],"doi":"10.1007/978-3-319-96145-3_5","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:04Z","publisher":"Springer","volume":10981,"month":"07","conference":{"start_date":"2018-07-14","location":"Oxford, UK","end_date":"2018-07-17","name":"CAV: Computer Aided Verification"},"date_created":"2018-12-11T11:44:57Z","status":"public","intvolume":"     10981","isi":1,"publist_id":"7761","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2018","citation":{"apa":"Kragl, B., &#38; Qadeer, S. (2018). Layered Concurrent Programs (Vol. 10981, pp. 79–102). Presented at the CAV: Computer Aided Verification, Oxford, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_5\">https://doi.org/10.1007/978-3-319-96145-3_5</a>","mla":"Kragl, Bernhard, and Shaz Qadeer. <i>Layered Concurrent Programs</i>. Vol. 10981, Springer, 2018, pp. 79–102, doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_5\">10.1007/978-3-319-96145-3_5</a>.","ama":"Kragl B, Qadeer S. Layered Concurrent Programs. In: Vol 10981. Springer; 2018:79-102. doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_5\">10.1007/978-3-319-96145-3_5</a>","ieee":"B. Kragl and S. Qadeer, “Layered Concurrent Programs,” presented at the CAV: Computer Aided Verification, Oxford, UK, 2018, vol. 10981, pp. 79–102.","ista":"Kragl B, Qadeer S. 2018. Layered Concurrent Programs. CAV: Computer Aided Verification, LNCS, vol. 10981, 79–102.","short":"B. Kragl, S. Qadeer, in:, Springer, 2018, pp. 79–102.","chicago":"Kragl, Bernhard, and Shaz Qadeer. “Layered Concurrent Programs,” 10981:79–102. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_5\">https://doi.org/10.1007/978-3-319-96145-3_5</a>."},"quality_controlled":"1","author":[{"first_name":"Bernhard","last_name":"Kragl","orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Shaz","last_name":"Qadeer","full_name":"Qadeer, Shaz"}],"project":[{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"abstract":[{"text":"We present layered concurrent programs, a compact and expressive notation for specifying refinement proofs of concurrent programs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. These programs are expressed in the ordinary syntax of imperative concurrent programs using gated atomic actions, sequencing, choice, and (recursive) procedure calls. Each concurrent program is automatically extracted from the layered program. We reduce refinement to the safety of a sequence of concurrent checker programs, one each to justify the connection between every two consecutive concurrent programs. These checker programs are also automatically extracted from the layered program. Layered concurrent programs have been implemented in the CIVL verifier which has been successfully used for the verification of several complex concurrent programs.","lang":"eng"}],"publication_status":"published","title":"Layered Concurrent Programs","_id":"160","oa":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8332"}]},"ddc":["000"]},{"department":[{"_id":"GaTk"},{"_id":"CaGu"}],"has_accepted_license":"1","doi":"10.1038/s41467-018-05417-9","language":[{"iso":"eng"}],"ec_funded":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","day":"30","oa_version":"Published Version","type":"journal_article","date_updated":"2024-02-21T13:45:39Z","scopus_import":"1","file":[{"date_created":"2018-12-17T16:44:28Z","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1043205,"file_id":"5728","date_updated":"2020-07-14T12:45:06Z","access_level":"open_access","checksum":"3ba7ab27b27723c7dcf633e8fc1f8f18","file_name":"2018_NatureComm_DeMartino.pdf"}],"external_id":{"isi":["000440149300021"]},"date_published":"2018-07-30T00:00:00Z","_id":"161","ddc":["570"],"oa":1,"related_material":{"record":[{"id":"5587","relation":"popular_science","status":"public"}]},"title":"Statistical mechanics for metabolic networks during steady state growth","publication":"Nature Communications","abstract":[{"text":"Which properties of metabolic networks can be derived solely from stoichiometry? Predictive results have been obtained by flux balance analysis (FBA), by postulating that cells set metabolic fluxes to maximize growth rate. Here we consider a generalization of FBA to single-cell level using maximum entropy modeling, which we extend and test experimentally. Specifically, we define for Escherichia coli metabolism a flux distribution that yields the experimental growth rate: the model, containing FBA as a limit, provides a better match to measured fluxes and it makes a wide range of predictions: on flux variability, regulation, and correlations; on the relative importance of stoichiometry vs. optimization; on scaling relations for growth rate distributions. We validate the latter here with single-cell data at different sub-inhibitory antibiotic concentrations. The model quantifies growth optimization as emerging from the interplay of competitive dynamics in the population and regulation of metabolism at the level of single cells.","lang":"eng"}],"publication_status":"published","project":[{"grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","author":[{"full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","last_name":"De Martino","first_name":"Daniele"},{"full_name":"Mc, Andersson Anna","first_name":"Andersson Anna","last_name":"Mc"},{"orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","first_name":"Tobias"},{"first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","first_name":"Gasper"}],"citation":{"ama":"De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. Statistical mechanics for metabolic networks during steady state growth. <i>Nature Communications</i>. 2018;9(1). doi:<a href=\"https://doi.org/10.1038/s41467-018-05417-9\">10.1038/s41467-018-05417-9</a>","ieee":"D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkačik, “Statistical mechanics for metabolic networks during steady state growth,” <i>Nature Communications</i>, vol. 9, no. 1. Springer Nature, 2018.","chicago":"De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet, and Gašper Tkačik. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” <i>Nature Communications</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41467-018-05417-9\">https://doi.org/10.1038/s41467-018-05417-9</a>.","short":"D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkačik, Nature Communications 9 (2018).","ista":"De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. 2018. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 9(1), 2988.","apa":"De Martino, D., Mc, A. A., Bergmiller, T., Guet, C. C., &#38; Tkačik, G. (2018). Statistical mechanics for metabolic networks during steady state growth. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-018-05417-9\">https://doi.org/10.1038/s41467-018-05417-9</a>","mla":"De Martino, Daniele, et al. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” <i>Nature Communications</i>, vol. 9, no. 1, 2988, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s41467-018-05417-9\">10.1038/s41467-018-05417-9</a>."},"year":"2018","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"isi":1,"publist_id":"7760","intvolume":"         9","status":"public","article_number":"2988","month":"07","date_created":"2018-12-11T11:44:57Z","issue":"1","volume":9,"publisher":"Springer Nature","file_date_updated":"2020-07-14T12:45:06Z"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","day":"13","date_updated":"2023-09-18T09:29:07Z","type":"journal_article","oa_version":"Published Version","language":[{"iso":"eng"}],"doi":"10.7554/eLife.34465","has_accepted_license":"1","department":[{"_id":"AnKi"}],"ec_funded":1,"date_published":"2018-06-13T00:00:00Z","file":[{"file_size":9816484,"creator":"dernst","content_type":"application/pdf","relation":"main_file","date_created":"2018-12-17T16:41:58Z","checksum":"da2378cdcf6b5461dcde194e4d608343","file_name":"2018_eLife_Kaucka.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:07Z","file_id":"5727"}],"external_id":{"isi":["000436227500001"]},"scopus_import":"1","quality_controlled":"1","author":[{"full_name":"Kaucka, Marketa","last_name":"Kaucka","first_name":"Marketa"},{"last_name":"Petersen","first_name":"Julian","full_name":"Petersen, Julian"},{"first_name":"Marketa","last_name":"Tesarova","full_name":"Tesarova, Marketa"},{"last_name":"Szarowska","first_name":"Bara","full_name":"Szarowska, Bara"},{"full_name":"Kastriti, Maria","first_name":"Maria","last_name":"Kastriti"},{"last_name":"Xie","first_name":"Meng","full_name":"Xie, Meng"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","last_name":"Kicheva","first_name":"Anna"},{"full_name":"Annusver, Karl","first_name":"Karl","last_name":"Annusver"},{"last_name":"Kasper","first_name":"Maria","full_name":"Kasper, Maria"},{"full_name":"Symmons, Orsolya","last_name":"Symmons","first_name":"Orsolya"},{"full_name":"Pan, Leslie","first_name":"Leslie","last_name":"Pan"},{"full_name":"Spitz, Francois","last_name":"Spitz","first_name":"Francois"},{"full_name":"Kaiser, Jozef","last_name":"Kaiser","first_name":"Jozef"},{"full_name":"Hovorakova, Maria","last_name":"Hovorakova","first_name":"Maria"},{"full_name":"Zikmund, Tomas","first_name":"Tomas","last_name":"Zikmund"},{"full_name":"Sunadome, Kazunori","last_name":"Sunadome","first_name":"Kazunori"},{"first_name":"Michael P","last_name":"Matise","full_name":"Matise, Michael P"},{"full_name":"Wang, Hui","first_name":"Hui","last_name":"Wang"},{"full_name":"Marklund, Ulrika","first_name":"Ulrika","last_name":"Marklund"},{"full_name":"Abdo, Hind","last_name":"Abdo","first_name":"Hind"},{"full_name":"Ernfors, Patrik","last_name":"Ernfors","first_name":"Patrik"},{"first_name":"Pascal","last_name":"Maire","full_name":"Maire, Pascal"},{"last_name":"Wurmser","first_name":"Maud","full_name":"Wurmser, Maud"},{"full_name":"Chagin, Andrei S","last_name":"Chagin","first_name":"Andrei S"},{"first_name":"Kaj","last_name":"Fried","full_name":"Fried, Kaj"},{"first_name":"Igor","last_name":"Adameyko","full_name":"Adameyko, Igor"}],"citation":{"ama":"Kaucka M, Petersen J, Tesarova M, et al. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. <i>eLife</i>. 2018;7. doi:<a href=\"https://doi.org/10.7554/eLife.34465\">10.7554/eLife.34465</a>","ieee":"M. Kaucka <i>et al.</i>, “Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage,” <i>eLife</i>, vol. 7. eLife Sciences Publications, 2018.","chicago":"Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria Kastriti, Meng Xie, Anna Kicheva, et al. “Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” <i>ELife</i>. eLife Sciences Publications, 2018. <a href=\"https://doi.org/10.7554/eLife.34465\">https://doi.org/10.7554/eLife.34465</a>.","short":"M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M. Kastriti, M. Xie, A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M. Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo, P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, ELife 7 (2018).","ista":"Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti M, Xie M, Kicheva A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser M, Chagin AS, Fried K, Adameyko I. 2018. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. eLife. 7, e34465.","apa":"Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M., Xie, M., … Adameyko, I. (2018). Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.34465\">https://doi.org/10.7554/eLife.34465</a>","mla":"Kaucka, Marketa, et al. “Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” <i>ELife</i>, vol. 7, e34465, eLife Sciences Publications, 2018, doi:<a href=\"https://doi.org/10.7554/eLife.34465\">10.7554/eLife.34465</a>."},"year":"2018","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9838"}]},"ddc":["571"],"_id":"162","publication":"eLife","title":"Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage","publication_status":"published","abstract":[{"lang":"eng","text":"Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here, we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts."}],"project":[{"_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020","name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037"}],"volume":7,"publisher":"eLife Sciences Publications","file_date_updated":"2020-07-14T12:45:07Z","publist_id":"7759","isi":1,"intvolume":"         7","status":"public","article_number":"e34465","date_created":"2018-12-11T11:44:57Z","month":"06"},{"citation":{"ieee":"S. Reipert <i>et al.</i>, “Agitation modules: Flexible means to accelerate automated freeze substitution,” <i>Journal of Histochemistry and Cytochemistry</i>, vol. 66, no. 12. SAGE Publications, pp. 903–921, 2018.","ama":"Reipert S, Goldammer H, Richardson C, et al. Agitation modules: Flexible means to accelerate automated freeze substitution. <i>Journal of Histochemistry and Cytochemistry</i>. 2018;66(12):903-921. doi:<a href=\"https://doi.org/10.1369/0022155418786698\">10.1369/0022155418786698</a>","ista":"Reipert S, Goldammer H, Richardson C, Goldberg M, Hawkins T, Saeckl E, Kaufmann W, Antreich S, Stierhof Y. 2018. Agitation modules: Flexible means to accelerate automated freeze substitution. Journal of Histochemistry and Cytochemistry. 66(12), 903–921.","short":"S. Reipert, H. Goldammer, C. Richardson, M. Goldberg, T. Hawkins, E. Saeckl, W. Kaufmann, S. Antreich, Y. Stierhof, Journal of Histochemistry and Cytochemistry 66 (2018) 903–921.","chicago":"Reipert, Siegfried, Helmuth Goldammer, Christine Richardson, Martin Goldberg, Timothy Hawkins, Elena Saeckl, Walter Kaufmann, Sebastian Antreich, and York Stierhof. “Agitation Modules: Flexible Means to Accelerate Automated Freeze Substitution.” <i>Journal of Histochemistry and Cytochemistry</i>. SAGE Publications, 2018. <a href=\"https://doi.org/10.1369/0022155418786698\">https://doi.org/10.1369/0022155418786698</a>.","mla":"Reipert, Siegfried, et al. “Agitation Modules: Flexible Means to Accelerate Automated Freeze Substitution.” <i>Journal of Histochemistry and Cytochemistry</i>, vol. 66, no. 12, SAGE Publications, 2018, pp. 903–21, doi:<a href=\"https://doi.org/10.1369/0022155418786698\">10.1369/0022155418786698</a>.","apa":"Reipert, S., Goldammer, H., Richardson, C., Goldberg, M., Hawkins, T., Saeckl, E., … Stierhof, Y. (2018). Agitation modules: Flexible means to accelerate automated freeze substitution. <i>Journal of Histochemistry and Cytochemistry</i>. SAGE Publications. <a href=\"https://doi.org/10.1369/0022155418786698\">https://doi.org/10.1369/0022155418786698</a>"},"main_file_link":[{"url":"https://doi.org/10.1369/0022155418786698","open_access":"1"}],"quality_controlled":"1","author":[{"full_name":"Reipert, Siegfried","first_name":"Siegfried","last_name":"Reipert"},{"last_name":"Goldammer","first_name":"Helmuth","full_name":"Goldammer, Helmuth"},{"last_name":"Richardson","first_name":"Christine","full_name":"Richardson, Christine"},{"first_name":"Martin","last_name":"Goldberg","full_name":"Goldberg, Martin"},{"last_name":"Hawkins","first_name":"Timothy","full_name":"Hawkins, Timothy"},{"first_name":"Elena","last_name":"Hollergschwandtner","full_name":"Hollergschwandtner, Elena","id":"3C054040-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kaufmann","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315"},{"last_name":"Antreich","first_name":"Sebastian","full_name":"Antreich, Sebastian"},{"full_name":"Stierhof, York","last_name":"Stierhof","first_name":"York"}],"year":"2018","pmid":1,"title":"Agitation modules: Flexible means to accelerate automated freeze substitution","publication":"Journal of Histochemistry and Cytochemistry","_id":"163","oa":1,"abstract":[{"lang":"eng","text":"For ultrafast fixation of biological samples to avoid artifacts, high-pressure freezing (HPF) followed by freeze substitution (FS) is preferred over chemical fixation at room temperature. After HPF, samples are maintained at low temperature during dehydration and fixation, while avoiding damaging recrystallization. This is a notoriously slow process. McDonald and Webb demonstrated, in 2011, that sample agitation during FS dramatically reduces the necessary time. Then, in 2015, we (H.G. and S.R.) introduced an agitation module into the cryochamber of an automated FS unit and demonstrated that the preparation of algae could be shortened from days to a couple of hours. We argued that variability in the processing, reproducibility, and safety issues are better addressed using automated FS units. For dissemination, we started low-cost manufacturing of agitation modules for two of the most widely used FS units, the Automatic Freeze Substitution Systems, AFS(1) and AFS2, from Leica Microsystems, using three dimensional (3D)-printing of the major components. To test them, several labs independently used the modules on a wide variety of specimens that had previously been processed by manual agitation, or without agitation. We demonstrate that automated processing with sample agitation saves time, increases flexibility with respect to sample requirements and protocols, and produces data of at least as good quality as other approaches."}],"publication_status":"published","volume":66,"issue":"12","publisher":"SAGE Publications","article_type":"original","intvolume":"        66","isi":1,"month":"12","date_created":"2018-12-11T11:44:57Z","status":"public","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","date_updated":"2023-10-17T08:42:24Z","type":"journal_article","day":"01","department":[{"_id":"RySh"},{"_id":"EM-Fac"}],"doi":"10.1369/0022155418786698","language":[{"iso":"eng"}],"external_id":{"isi":["000452277700005"],"pmid":["29969056"]},"date_published":"2018-12-01T00:00:00Z","page":"903-921","scopus_import":"1","publication_identifier":{"issn":["0022-1554"]}},{"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"15","oa_version":"Published Version","date_updated":"2023-09-11T12:59:28Z","type":"journal_article","has_accepted_license":"1","department":[{"_id":"BjHo"}],"doi":"10.1103/PhysRevFluids.3.103302","language":[{"iso":"eng"}],"ec_funded":1,"external_id":{"isi":["000447311500001"]},"file":[{"date_created":"2018-12-12T10:10:14Z","relation":"main_file","content_type":"application/pdf","creator":"system","file_size":1409040,"date_updated":"2020-07-14T12:45:12Z","file_id":"4800","access_level":"open_access","checksum":"e1445be33e8165114e96246275600750","file_name":"IST-2018-1061-v1+1_PhysRevFluids.3.103302.pdf"}],"date_published":"2018-10-15T00:00:00Z","scopus_import":"1","author":[{"last_name":"Varshney","first_name":"Atul","full_name":"Varshney, Atul","orcid":"0000-0002-3072-5999","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Victor","last_name":"Steinberg","full_name":"Steinberg, Victor"}],"quality_controlled":"1","citation":{"mla":"Varshney, Atul, and Victor Steinberg. “Drag Enhancement and Drag Reduction in Viscoelastic Flow.” <i>Physical Review Fluids</i>, vol. 3, no. 10, 103302, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.3.103302\">10.1103/PhysRevFluids.3.103302</a>.","apa":"Varshney, A., &#38; Steinberg, V. (2018). Drag enhancement and drag reduction in viscoelastic flow. <i>Physical Review Fluids</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevFluids.3.103302\">https://doi.org/10.1103/PhysRevFluids.3.103302</a>","ama":"Varshney A, Steinberg V. Drag enhancement and drag reduction in viscoelastic flow. <i>Physical Review Fluids</i>. 2018;3(10). doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.3.103302\">10.1103/PhysRevFluids.3.103302</a>","ieee":"A. Varshney and V. Steinberg, “Drag enhancement and drag reduction in viscoelastic flow,” <i>Physical Review Fluids</i>, vol. 3, no. 10. American Physical Society, 2018.","ista":"Varshney A, Steinberg V. 2018. Drag enhancement and drag reduction in viscoelastic flow. Physical Review Fluids. 3(10), 103302.","short":"A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).","chicago":"Varshney, Atul, and Victor Steinberg. “Drag Enhancement and Drag Reduction in Viscoelastic Flow.” <i>Physical Review Fluids</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevFluids.3.103302\">https://doi.org/10.1103/PhysRevFluids.3.103302</a>."},"year":"2018","_id":"17","oa":1,"ddc":["532"],"title":"Drag enhancement and drag reduction in viscoelastic flow","publication":"Physical Review Fluids","abstract":[{"text":"Creeping flow of polymeric fluid without inertia exhibits elastic instabilities and elastic turbulence accompanied by drag enhancement due to elastic stress produced by flow-stretched polymers. However, in inertia-dominated flow at high Re and low fluid elasticity El, a reduction in turbulent frictional drag is caused by an intricate competition between inertial and elastic stresses. Here we explore the effect of inertia on the stability of viscoelastic flow in a broad range of control parameters El and (Re,Wi). We present the stability diagram of observed flow regimes in Wi-Re coordinates and find that the instabilities' onsets show an unexpectedly nonmonotonic dependence on El. Further, three distinct regions in the diagram are identified based on El. Strikingly, for high-elasticity fluids we discover a complete relaminarization of flow at Reynolds number in the range of 1 to 10, different from a well-known turbulent drag reduction. These counterintuitive effects may be explained by a finite polymer extensibility and a suppression of vorticity at high Wi. Our results call for further theoretical and numerical development to uncover the role of inertial effect on elastic turbulence in a viscoelastic flow.","lang":"eng"}],"publication_status":"published","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"pubrep_id":"1061","issue":"10","volume":3,"publisher":"American Physical Society","file_date_updated":"2020-07-14T12:45:12Z","isi":1,"publist_id":"8038","intvolume":"         3","status":"public","article_number":"103302 ","month":"10","date_created":"2018-12-11T11:44:11Z"},{"department":[{"_id":"VlKo"}],"language":[{"iso":"eng"}],"oa_version":"Preprint","date_updated":"2023-09-19T14:46:18Z","type":"journal_article","day":"01","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","arxiv":1,"scopus_import":"1","publication_identifier":{"issn":["0381-7032"]},"external_id":{"isi":["000446809500022"],"arxiv":["1405.7828"]},"date_published":"2018-10-01T00:00:00Z","page":"269 - 304","abstract":[{"text":"An N-superconcentrator is a directed, acyclic graph with N input nodes and N output nodes such that every subset of the inputs and every subset of the outputs of same cardinality can be connected by node-disjoint paths. It is known that linear-size and bounded-degree superconcentrators exist. We prove the existence of such superconcentrators with asymptotic density 25.3 (where the density is the number of edges divided by N). The previously best known densities were 28 [12] and 27.4136 [17].","lang":"eng"}],"publication_status":"published","publication":"Ars Combinatoria","title":"Superconcentrators of density 25.3","_id":"18","oa":1,"year":"2018","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1405.7828"}],"citation":{"ieee":"V. Kolmogorov and M. Rolinek, “Superconcentrators of density 25.3,” <i>Ars Combinatoria</i>, vol. 141, no. 10. Charles Babbage Research Centre, pp. 269–304, 2018.","ama":"Kolmogorov V, Rolinek M. Superconcentrators of density 25.3. <i>Ars Combinatoria</i>. 2018;141(10):269-304.","chicago":"Kolmogorov, Vladimir, and Michal Rolinek. “Superconcentrators of Density 25.3.” <i>Ars Combinatoria</i>. Charles Babbage Research Centre, 2018.","short":"V. Kolmogorov, M. Rolinek, Ars Combinatoria 141 (2018) 269–304.","ista":"Kolmogorov V, Rolinek M. 2018. Superconcentrators of density 25.3. Ars Combinatoria. 141(10), 269–304.","apa":"Kolmogorov, V., &#38; Rolinek, M. (2018). Superconcentrators of density 25.3. <i>Ars Combinatoria</i>. Charles Babbage Research Centre.","mla":"Kolmogorov, Vladimir, and Michal Rolinek. “Superconcentrators of Density 25.3.” <i>Ars Combinatoria</i>, vol. 141, no. 10, Charles Babbage Research Centre, 2018, pp. 269–304."},"quality_controlled":"1","author":[{"full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","first_name":"Vladimir"},{"last_name":"Rolinek","first_name":"Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","full_name":"Rolinek, Michal"}],"month":"10","date_created":"2018-12-11T11:44:11Z","status":"public","intvolume":"       141","isi":1,"publist_id":"8037","publisher":"Charles Babbage Research Centre","volume":141,"issue":"10"},{"page":"79 - 116","external_id":{"arxiv":["1705.10676"]},"file":[{"content_type":"application/pdf","creator":"dernst","file_size":843938,"date_created":"2018-12-17T16:38:18Z","relation":"main_file","access_level":"open_access","checksum":"1ba7cccdf3900f42c4f715ae75d6813c","file_name":"2018_JournaldeLecoleMath_Lewi.pdf","date_updated":"2020-07-14T12:45:16Z","file_id":"5726"}],"date_published":"2018-07-01T00:00:00Z","arxiv":1,"scopus_import":"1","publication_identifier":{"eissn":["2270-518X"],"issn":["2429-7100"]},"day":"01","oa_version":"Published Version","type":"journal_article","date_updated":"2023-10-17T08:05:28Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European\r\nUnion’s Horizon 2020 research and innovation programme (grant agreement 694227 for R.S. and MDFT 725528 for M.L.). Financial support by the Austrian Science Fund (FWF), project No P 27533-N27 (R.S.) and by the US National Science Foundation, grant No PHY12-1265118 (E.H.L.) are gratefully acknowledged.","department":[{"_id":"RoSe"}],"has_accepted_license":"1","license":"https://creativecommons.org/licenses/by-nd/4.0/","doi":"10.5802/jep.64","language":[{"iso":"eng"}],"ec_funded":1,"article_type":"original","publisher":"Ecole Polytechnique","file_date_updated":"2020-07-14T12:45:16Z","volume":5,"status":"public","month":"07","date_created":"2018-12-11T11:45:03Z","publist_id":"7741","intvolume":"         5","year":"2018","tmp":{"name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","image":"/image/cc_by_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","short":"CC BY-ND (4.0)"},"author":[{"full_name":"Lewi, Mathieu","last_name":"Lewi","first_name":"Mathieu"},{"last_name":"Lieb","first_name":"Élliott","full_name":"Lieb, Élliott"},{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert"}],"quality_controlled":"1","citation":{"mla":"Lewi, Mathieu, et al. “Statistical Mechanics of the Uniform Electron Gas.” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>, vol. 5, Ecole Polytechnique, 2018, pp. 79–116, doi:<a href=\"https://doi.org/10.5802/jep.64\">10.5802/jep.64</a>.","apa":"Lewi, M., Lieb, É., &#38; Seiringer, R. (2018). Statistical mechanics of the uniform electron gas. <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. Ecole Polytechnique. <a href=\"https://doi.org/10.5802/jep.64\">https://doi.org/10.5802/jep.64</a>","ieee":"M. Lewi, É. Lieb, and R. Seiringer, “Statistical mechanics of the uniform electron gas,” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>, vol. 5. Ecole Polytechnique, pp. 79–116, 2018.","ama":"Lewi M, Lieb É, Seiringer R. Statistical mechanics of the uniform electron gas. <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. 2018;5:79-116. doi:<a href=\"https://doi.org/10.5802/jep.64\">10.5802/jep.64</a>","ista":"Lewi M, Lieb É, Seiringer R. 2018. Statistical mechanics of the uniform electron gas. Journal de l’Ecole Polytechnique - Mathematiques. 5, 79–116.","chicago":"Lewi, Mathieu, Élliott Lieb, and Robert Seiringer. “Statistical Mechanics of the Uniform Electron Gas.” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. Ecole Polytechnique, 2018. <a href=\"https://doi.org/10.5802/jep.64\">https://doi.org/10.5802/jep.64</a>.","short":"M. Lewi, É. Lieb, R. Seiringer, Journal de l’Ecole Polytechnique - Mathematiques 5 (2018) 79–116."},"abstract":[{"text":"In this paper we define and study the classical Uniform Electron Gas (UEG), a system of infinitely many electrons whose density is constant everywhere in space. The UEG is defined differently from Jellium, which has a positive constant background but no constraint on the density. We prove that the UEG arises in Density Functional Theory in the limit of a slowly varying density, minimizing the indirect Coulomb energy. We also construct the quantum UEG and compare it to the classical UEG at low density.","lang":"eng"}],"publication_status":"published","project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227"},{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"_id":"180","oa":1,"ddc":["510"],"publication":"Journal de l'Ecole Polytechnique - Mathematiques","title":"Statistical mechanics of the uniform electron gas"},{"project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"M02080","name":"Structured Non-Hermitian Random Matrices","call_identifier":"FWF","_id":"258F40A4-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","text":"We consider large random matrices X with centered, independent entries but possibly di erent variances. We compute the normalized trace of f(X)g(X∗) for f, g functions analytic on the spectrum of X. We use these results to compute the long time asymptotics for systems of coupled di erential equations with random coe cients. We show that when the coupling is critical, the norm squared of the solution decays like t−1/2."}],"publication_status":"published","title":"Power law decay for systems of randomly coupled differential equations","publication":"SIAM Journal on Mathematical Analysis","_id":"181","oa":1,"year":"2018","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.01546"}],"citation":{"chicago":"Erdös, László, Torben H Krüger, and David T Renfrew. “Power Law Decay for Systems of Randomly Coupled Differential Equations.” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics , 2018. <a href=\"https://doi.org/10.1137/17M1143125\">https://doi.org/10.1137/17M1143125</a>.","short":"L. Erdös, T.H. Krüger, D.T. Renfrew, SIAM Journal on Mathematical Analysis 50 (2018) 3271–3290.","ista":"Erdös L, Krüger TH, Renfrew DT. 2018. Power law decay for systems of randomly coupled differential equations. SIAM Journal on Mathematical Analysis. 50(3), 3271–3290.","ama":"Erdös L, Krüger TH, Renfrew DT. Power law decay for systems of randomly coupled differential equations. <i>SIAM Journal on Mathematical Analysis</i>. 2018;50(3):3271-3290. doi:<a href=\"https://doi.org/10.1137/17M1143125\">10.1137/17M1143125</a>","ieee":"L. Erdös, T. H. Krüger, and D. T. Renfrew, “Power law decay for systems of randomly coupled differential equations,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 50, no. 3. Society for Industrial and Applied Mathematics , pp. 3271–3290, 2018.","apa":"Erdös, L., Krüger, T. H., &#38; Renfrew, D. T. (2018). Power law decay for systems of randomly coupled differential equations. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics . <a href=\"https://doi.org/10.1137/17M1143125\">https://doi.org/10.1137/17M1143125</a>","mla":"Erdös, László, et al. “Power Law Decay for Systems of Randomly Coupled Differential Equations.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 50, no. 3, Society for Industrial and Applied Mathematics , 2018, pp. 3271–90, doi:<a href=\"https://doi.org/10.1137/17M1143125\">10.1137/17M1143125</a>."},"quality_controlled":"1","author":[{"orcid":"0000-0001-5366-9603","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","last_name":"Erdös"},{"first_name":"Torben H","last_name":"Krüger","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David T","last_name":"Renfrew","orcid":"0000-0003-3493-121X","full_name":"Renfrew, David T","id":"4845BF6A-F248-11E8-B48F-1D18A9856A87"}],"month":"01","date_created":"2018-12-11T11:45:03Z","status":"public","intvolume":"        50","isi":1,"publist_id":"7740","publisher":"Society for Industrial and Applied Mathematics ","issue":"3","volume":50,"acknowledgement":"The work of the second author was also partially supported by the Hausdorff Center of Mathematics.","ec_funded":1,"department":[{"_id":"LaEr"}],"doi":"10.1137/17M1143125","language":[{"iso":"eng"}],"oa_version":"Published Version","type":"journal_article","date_updated":"2023-09-15T12:05:52Z","day":"01","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","arxiv":1,"scopus_import":"1","external_id":{"isi":["000437018500032"],"arxiv":["1708.01546"]},"date_published":"2018-01-01T00:00:00Z","page":"3271 - 3290"},{"page":"177 - 186","date_published":"2018-04-11T00:00:00Z","file":[{"date_updated":"2020-07-14T12:45:17Z","file_id":"7833","access_level":"open_access","file_name":"2018_HSCC_Bakhirkin.pdf","checksum":"81eabc96430e84336ea88310ac0a1ad0","date_created":"2020-05-14T12:18:29Z","relation":"main_file","file_size":5900421,"content_type":"application/pdf","creator":"dernst"}],"external_id":{"isi":["000474781600020"]},"publication_identifier":{"isbn":["978-1-4503-5642-8 "]},"scopus_import":"1","alternative_title":["HSCC Proceedings"],"day":"11","date_updated":"2023-09-11T13:30:51Z","type":"conference","oa_version":"Submitted Version","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"doi":"10.1145/3178126.3178132","department":[{"_id":"ToHe"}],"has_accepted_license":"1","publisher":"ACM","file_date_updated":"2020-07-14T12:45:17Z","status":"public","date_created":"2018-12-11T11:45:04Z","month":"04","conference":{"start_date":"2018-04-11","location":"Porto, Portugal","end_date":"2018-04-13","name":"HSCC: Hybrid Systems: Computation and Control"},"publist_id":"7739","isi":1,"year":"2018","author":[{"last_name":"Bakhirkin","first_name":"Alexey","full_name":"Bakhirkin, Alexey"},{"last_name":"Ferrere","first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143"},{"first_name":"Oded","last_name":"Maler","full_name":"Maler, Oded"}],"quality_controlled":"1","citation":{"apa":"Bakhirkin, A., Ferrere, T., &#38; Maler, O. (2018). Efficient parametric identification for STL. In <i>Proceedings of the 21st International Conference on Hybrid Systems</i> (pp. 177–186). Porto, Portugal: ACM. <a href=\"https://doi.org/10.1145/3178126.3178132\">https://doi.org/10.1145/3178126.3178132</a>","mla":"Bakhirkin, Alexey, et al. “Efficient Parametric Identification for STL.” <i>Proceedings of the 21st International Conference on Hybrid Systems</i>, ACM, 2018, pp. 177–86, doi:<a href=\"https://doi.org/10.1145/3178126.3178132\">10.1145/3178126.3178132</a>.","ieee":"A. Bakhirkin, T. Ferrere, and O. Maler, “Efficient parametric identification for STL,” in <i>Proceedings of the 21st International Conference on Hybrid Systems</i>, Porto, Portugal, 2018, pp. 177–186.","ama":"Bakhirkin A, Ferrere T, Maler O. Efficient parametric identification for STL. In: <i>Proceedings of the 21st International Conference on Hybrid Systems</i>. ACM; 2018:177-186. doi:<a href=\"https://doi.org/10.1145/3178126.3178132\">10.1145/3178126.3178132</a>","short":"A. Bakhirkin, T. Ferrere, O. Maler, in:, Proceedings of the 21st International Conference on Hybrid Systems, ACM, 2018, pp. 177–186.","chicago":"Bakhirkin, Alexey, Thomas Ferrere, and Oded Maler. “Efficient Parametric Identification for STL.” In <i>Proceedings of the 21st International Conference on Hybrid Systems</i>, 177–86. ACM, 2018. <a href=\"https://doi.org/10.1145/3178126.3178132\">https://doi.org/10.1145/3178126.3178132</a>.","ista":"Bakhirkin A, Ferrere T, Maler O. 2018. Efficient parametric identification for STL. Proceedings of the 21st International Conference on Hybrid Systems. HSCC: Hybrid Systems: Computation and Control, HSCC Proceedings, , 177–186."},"publication_status":"published","abstract":[{"text":"We describe a new algorithm for the parametric identification problem for signal temporal logic (STL), stated as follows. Given a densetime real-valued signal w and a parameterized temporal logic formula φ, compute the subset of the parameter space that renders the formula satisfied by the signal. Unlike previous solutions, which were based on search in the parameter space or quantifier elimination, our procedure works recursively on φ and computes the evolution over time of the set of valid parameter assignments. This procedure is similar to that of monitoring or computing the robustness of φ relative to w. Our implementation and experiments demonstrate that this approach can work well in practice.","lang":"eng"}],"project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"ddc":["000"],"oa":1,"_id":"182","title":"Efficient parametric identification for STL","publication":"Proceedings of the 21st International Conference on Hybrid Systems"},{"page":"197 - 206","date_published":"2018-04-11T00:00:00Z","external_id":{"isi":["000474781600022"]},"scopus_import":"1","alternative_title":["HSCC Proceedings"],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"11","date_updated":"2023-09-13T08:48:46Z","type":"conference","oa_version":"None","language":[{"iso":"eng"}],"doi":"10.1145/3178126.3178131","department":[{"_id":"ToHe"}],"acknowledgement":"This work was partially supported by the Austrian Science Fund (FWF) under grants S11402-N23 and S11405-N23 (RiSE/SHiNE), the CPS/IoT project (HRSM), the EU ICT COST Action IC1402 on Run-time Verification beyond Monitoring (ARVI), the AMASS project (ECSEL 692474), and the ENABLE-S3 project (ECSEL 692455). The CPS/IoT project receives support from the Austrian government through the Federal Ministry of Science, Research and Economy (BMWFW) in the funding program Hochschulraum-Strukturmittel (HRSM) 2016. The ECSEL Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and Austria, Denmark, Germany, Finland, Czech Republic, Italy, Spain, Portugal, Poland, Ireland, Belgium, France, Netherlands, United Kingdom, Slovakia, Norway.","publisher":"Association for Computing Machinery, Inc","publist_id":"7738","isi":1,"status":"public","date_created":"2018-12-11T11:45:04Z","month":"04","conference":{"end_date":"2018-04-13","name":"HSCC: Hybrid Systems: Computation and Control","location":"Porto, Portugal","start_date":"2018-04-11"},"author":[{"last_name":"Bartocci","first_name":"Ezio","full_name":"Bartocci, Ezio"},{"first_name":"Thomas","last_name":"Ferrere","full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Manjunath, Niveditha","first_name":"Niveditha","last_name":"Manjunath"},{"full_name":"Nickovic, Dejan","last_name":"Nickovic","first_name":"Dejan"}],"quality_controlled":"1","citation":{"apa":"Bartocci, E., Ferrere, T., Manjunath, N., &#38; Nickovic, D. (2018). Localizing faults in simulink/stateflow models with STL (pp. 197–206). Presented at the HSCC: Hybrid Systems: Computation and Control, Porto, Portugal: Association for Computing Machinery, Inc. <a href=\"https://doi.org/10.1145/3178126.3178131\">https://doi.org/10.1145/3178126.3178131</a>","mla":"Bartocci, Ezio, et al. <i>Localizing Faults in Simulink/Stateflow Models with STL</i>. Association for Computing Machinery, Inc, 2018, pp. 197–206, doi:<a href=\"https://doi.org/10.1145/3178126.3178131\">10.1145/3178126.3178131</a>.","chicago":"Bartocci, Ezio, Thomas Ferrere, Niveditha Manjunath, and Dejan Nickovic. “Localizing Faults in Simulink/Stateflow Models with STL,” 197–206. Association for Computing Machinery, Inc, 2018. <a href=\"https://doi.org/10.1145/3178126.3178131\">https://doi.org/10.1145/3178126.3178131</a>.","short":"E. Bartocci, T. Ferrere, N. Manjunath, D. Nickovic, in:, Association for Computing Machinery, Inc, 2018, pp. 197–206.","ista":"Bartocci E, Ferrere T, Manjunath N, Nickovic D. 2018. Localizing faults in simulink/stateflow models with STL. HSCC: Hybrid Systems: Computation and Control, HSCC Proceedings, , 197–206.","ieee":"E. Bartocci, T. Ferrere, N. Manjunath, and D. Nickovic, “Localizing faults in simulink/stateflow models with STL,” presented at the HSCC: Hybrid Systems: Computation and Control, Porto, Portugal, 2018, pp. 197–206.","ama":"Bartocci E, Ferrere T, Manjunath N, Nickovic D. Localizing faults in simulink/stateflow models with STL. In: Association for Computing Machinery, Inc; 2018:197-206. doi:<a href=\"https://doi.org/10.1145/3178126.3178131\">10.1145/3178126.3178131</a>"},"year":"2018","_id":"183","title":"Localizing faults in simulink/stateflow models with STL","publication_status":"published","abstract":[{"text":"Fault-localization is considered to be a very tedious and time-consuming activity in the design of complex Cyber-Physical Systems (CPS). This laborious task essentially requires expert knowledge of the system in order to discover the cause of the fault. In this context, we propose a new procedure that AIDS designers in debugging Simulink/Stateflow hybrid system models, guided by Signal Temporal Logic (STL) specifications. The proposed method relies on three main ingredients: (1) a monitoring and a trace diagnostics procedure that checks whether a tested behavior satisfies or violates an STL specification, localizes time segments and interfaces variables contributing to the property violations; (2) a slicing procedure that maps these observable behavior segments to the internal states and transitions of the Simulink model; and (3) a spectrum-based fault-localization method that combines the previous analysis from multiple tests to identify the internal states and/or transitions that are the most likely to explain the fault. We demonstrate the applicability of our approach on two Simulink models from the automotive and the avionics domain.","lang":"eng"}],"project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}]},{"_id":"184","ddc":["516","000"],"oa":1,"related_material":{"record":[{"id":"7108","status":"public","relation":"later_version"}]},"title":"Shellability is NP-complete","abstract":[{"lang":"eng","text":"We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial complex is shellable is NP-hard, hence NP-complete. This resolves a question raised, e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d ≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible pure d-dimensional complexes."}],"publication_status":"published","quality_controlled":"1","author":[{"full_name":"Goaoc, Xavier","first_name":"Xavier","last_name":"Goaoc"},{"last_name":"Paták","first_name":"Pavel","full_name":"Paták, Pavel"},{"full_name":"Patakova, Zuzana","orcid":"0000-0002-3975-1683","id":"48B57058-F248-11E8-B48F-1D18A9856A87","last_name":"Patakova","first_name":"Zuzana"},{"last_name":"Tancer","first_name":"Martin","orcid":"0000-0002-1191-6714","full_name":"Tancer, Martin","id":"38AC689C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wagner","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"}],"citation":{"apa":"Goaoc, X., Paták, P., Patakova, Z., Tancer, M., &#38; Wagner, U. (2018). Shellability is NP-complete (Vol. 99, p. 41:1-41:16). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.41\">https://doi.org/10.4230/LIPIcs.SoCG.2018.41</a>","mla":"Goaoc, Xavier, et al. <i>Shellability Is NP-Complete</i>. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 41:1-41:16, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.41\">10.4230/LIPIcs.SoCG.2018.41</a>.","ieee":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “Shellability is NP-complete,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 41:1-41:16.","ama":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. Shellability is NP-complete. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:41:1-41:16. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.41\">10.4230/LIPIcs.SoCG.2018.41</a>","chicago":"Goaoc, Xavier, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Shellability Is NP-Complete,” 99:41:1-41:16. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.41\">https://doi.org/10.4230/LIPIcs.SoCG.2018.41</a>.","short":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 41:1-41:16.","ista":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. 2018. Shellability is NP-complete. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 41:1-41:16."},"year":"2018","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publist_id":"7736","intvolume":"        99","status":"public","conference":{"end_date":"2018-06-14","name":"SoCG: Symposium on Computational Geometry","location":"Budapest, Hungary","start_date":"2018-06-11"},"month":"06","date_created":"2018-12-11T11:45:04Z","volume":99,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file_date_updated":"2020-07-14T12:45:18Z","has_accepted_license":"1","department":[{"_id":"UlWa"}],"doi":"10.4230/LIPIcs.SoCG.2018.41","language":[{"iso":"eng"}],"acknowledgement":"Partially supported by the project EMBEDS II (CZ: 7AMB17FR029, FR: 38087RM) of Czech-French collaboration.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"11","oa_version":"Published Version","type":"conference","date_updated":"2023-09-06T11:10:57Z","scopus_import":1,"alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"page":"41:1 - 41:16","file":[{"file_size":718414,"content_type":"application/pdf","creator":"dernst","relation":"main_file","date_created":"2018-12-17T16:35:02Z","file_name":"2018_LIPIcs_Goaoc.pdf","checksum":"d12bdd60f04a57307867704b5f930afd","access_level":"open_access","file_id":"5725","date_updated":"2020-07-14T12:45:18Z"}],"date_published":"2018-06-11T00:00:00Z"},{"volume":99,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file_date_updated":"2020-07-14T12:45:19Z","publist_id":"7735","intvolume":"        99","article_number":"39","status":"public","date_created":"2018-12-11T11:45:04Z","month":"01","conference":{"start_date":"2018-06-11","location":"Budapest, Hungary","end_date":"2018-06-14","name":"SoCG: Symposium on Computational Geometry"},"author":[{"last_name":"Fulek","first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774"},{"full_name":"Kynčl, Jan","first_name":"Jan","last_name":"Kynčl"}],"quality_controlled":"1","citation":{"apa":"Fulek, R., &#38; Kynčl, J. (2018). Hanani-Tutte for approximating maps of graphs (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.39\">https://doi.org/10.4230/LIPIcs.SoCG.2018.39</a>","mla":"Fulek, Radoslav, and Jan Kynčl. <i>Hanani-Tutte for Approximating Maps of Graphs</i>. Vol. 99, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.39\">10.4230/LIPIcs.SoCG.2018.39</a>.","ama":"Fulek R, Kynčl J. Hanani-Tutte for approximating maps of graphs. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.39\">10.4230/LIPIcs.SoCG.2018.39</a>","ieee":"R. Fulek and J. Kynčl, “Hanani-Tutte for approximating maps of graphs,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","ista":"Fulek R, Kynčl J. 2018. Hanani-Tutte for approximating maps of graphs. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 39.","short":"R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","chicago":"Fulek, Radoslav, and Jan Kynčl. “Hanani-Tutte for Approximating Maps of Graphs,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.39\">https://doi.org/10.4230/LIPIcs.SoCG.2018.39</a>."},"year":"2018","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"ddc":["510"],"_id":"185","title":"Hanani-Tutte for approximating maps of graphs","publication_status":"published","abstract":[{"lang":"eng","text":"We resolve in the affirmative conjectures of A. Skopenkov and Repovš (1998), and M. Skopenkov (2003) generalizing the classical Hanani-Tutte theorem to the setting of approximating maps of graphs on 2-dimensional surfaces by embeddings. Our proof of this result is constructive and almost immediately implies an efficient algorithm for testing whether a given piecewise linear map of a graph in a surface is approximable by an embedding. More precisely, an instance of this problem consists of (i) a graph G whose vertices are partitioned into clusters and whose inter-cluster edges are partitioned into bundles, and (ii) a region R of a 2-dimensional compact surface M given as the union of a set of pairwise disjoint discs corresponding to the clusters and a set of pairwise disjoint &quot;pipes&quot; corresponding to the bundles, connecting certain pairs of these discs. We are to decide whether G can be embedded inside M so that the vertices in every cluster are drawn in the corresponding disc, the edges in every bundle pass only through its corresponding pipe, and every edge crosses the boundary of each disc at most once."}],"project":[{"call_identifier":"FWF","_id":"261FA626-B435-11E9-9278-68D0E5697425","name":"Eliminating intersections in drawings of graphs","grant_number":"M02281"}],"date_published":"2018-01-01T00:00:00Z","file":[{"creator":"dernst","content_type":"application/pdf","file_size":718857,"date_created":"2018-12-17T12:33:52Z","relation":"main_file","access_level":"open_access","checksum":"f1b94f1a75b37c414a1f61d59fb2cd4c","file_name":"2018_LIPIcs_Fulek.pdf","date_updated":"2020-07-14T12:45:19Z","file_id":"5701"}],"publication_identifier":{"isbn":["978-3-95977-066-8"]},"scopus_import":1,"alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","type":"conference","date_updated":"2021-01-12T06:53:36Z","oa_version":"Published Version","doi":"10.4230/LIPIcs.SoCG.2018.39","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"UlWa"}]},{"day":"11","date_updated":"2023-08-14T12:43:51Z","type":"conference","oa_version":"Submitted Version","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.4230/LIPIcs.SoCG.2018.40","language":[{"iso":"eng"}],"department":[{"_id":"UlWa"}],"page":"40.1 - 40.14","date_published":"2018-06-11T00:00:00Z","external_id":{"arxiv":["1803.05085"]},"arxiv":1,"scopus_import":"1","alternative_title":["LIPIcs"],"year":"2018","quality_controlled":"1","author":[{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","first_name":"Radoslav"},{"first_name":"Jan","last_name":"Kynčl","full_name":"Kynčl, Jan"}],"citation":{"ama":"Fulek R, Kynčl J. The ℤ2-Genus of Kuratowski minors. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:40.1-40.14. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.40\">10.4230/LIPIcs.SoCG.2018.40</a>","ieee":"R. Fulek and J. Kynčl, “The ℤ2-Genus of Kuratowski minors,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 40.1-40.14.","ista":"Fulek R, Kynčl J. 2018. The ℤ2-Genus of Kuratowski minors. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 40.1-40.14.","short":"R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14.","chicago":"Fulek, Radoslav, and Jan Kynčl. “The ℤ2-Genus of Kuratowski Minors,” 99:40.1-40.14. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.40\">https://doi.org/10.4230/LIPIcs.SoCG.2018.40</a>.","apa":"Fulek, R., &#38; Kynčl, J. (2018). The ℤ2-Genus of Kuratowski minors (Vol. 99, p. 40.1-40.14). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.40\">https://doi.org/10.4230/LIPIcs.SoCG.2018.40</a>","mla":"Fulek, Radoslav, and Jan Kynčl. <i>The ℤ2-Genus of Kuratowski Minors</i>. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.40\">10.4230/LIPIcs.SoCG.2018.40</a>."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.05085"}],"publication_status":"published","abstract":[{"lang":"eng","text":"A drawing of a graph on a surface is independently even if every pair of nonadjacent edges in the drawing crosses an even number of times. The ℤ2-genus of a graph G is the minimum g such that G has an independently even drawing on the orientable surface of genus g. An unpublished result by Robertson and Seymour implies that for every t, every graph of sufficiently large genus contains as a minor a projective t × t grid or one of the following so-called t-Kuratowski graphs: K3, t, or t copies of K5 or K3,3 sharing at most 2 common vertices. We show that the ℤ2-genus of graphs in these families is unbounded in t; in fact, equal to their genus. Together, this implies that the genus of a graph is bounded from above by a function of its ℤ2-genus, solving a problem posed by Schaefer and Štefankovič, and giving an approximate version of the Hanani-Tutte theorem on orientable surfaces."}],"project":[{"call_identifier":"FWF","_id":"261FA626-B435-11E9-9278-68D0E5697425","grant_number":"M02281","name":"Eliminating intersections in drawings of graphs"}],"related_material":{"record":[{"id":"11593","relation":"later_version","status":"public"}]},"oa":1,"_id":"186","title":"The ℤ2-Genus of Kuratowski minors","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","volume":99,"status":"public","date_created":"2018-12-11T11:45:05Z","month":"06","conference":{"end_date":"2018-06-14","name":"SoCG: Symposium on Computational Geometry","start_date":"2018-06-11","location":"Budapest, Hungary"},"publist_id":"7734","intvolume":"        99"},{"file":[{"content_type":"application/pdf","creator":"dernst","file_size":528018,"relation":"main_file","date_created":"2018-12-18T09:27:22Z","file_name":"2018_LIPIcs_Edelsbrunner_Osang.pdf","checksum":"d8c0533ad0018eb4ed1077475eb8fc18","access_level":"open_access","file_id":"5738","date_updated":"2020-07-14T12:45:19Z"}],"date_published":"2018-06-11T00:00:00Z","alternative_title":["LIPIcs"],"scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","type":"conference","date_updated":"2023-09-07T13:29:00Z","day":"11","department":[{"_id":"HeEd"}],"has_accepted_license":"1","doi":"10.4230/LIPIcs.SoCG.2018.34","language":[{"iso":"eng"}],"acknowledgement":"This work is partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","volume":99,"file_date_updated":"2020-07-14T12:45:19Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","intvolume":"        99","publist_id":"7732","month":"06","conference":{"start_date":"2018-06-11","location":"Budapest, Hungary","name":"SoCG: Symposium on Computational Geometry","end_date":"2018-06-14"},"date_created":"2018-12-11T11:45:05Z","article_number":"34","status":"public","citation":{"mla":"Edelsbrunner, Herbert, and Georg F. Osang. <i>The Multi-Cover Persistence of Euclidean Balls</i>. Vol. 99, 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.34\">10.4230/LIPIcs.SoCG.2018.34</a>.","apa":"Edelsbrunner, H., &#38; Osang, G. F. (2018). The multi-cover persistence of Euclidean balls (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.34\">https://doi.org/10.4230/LIPIcs.SoCG.2018.34</a>","ama":"Edelsbrunner H, Osang GF. The multi-cover persistence of Euclidean balls. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.34\">10.4230/LIPIcs.SoCG.2018.34</a>","ieee":"H. Edelsbrunner and G. F. Osang, “The multi-cover persistence of Euclidean balls,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","short":"H. Edelsbrunner, G.F. Osang, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","chicago":"Edelsbrunner, Herbert, and Georg F Osang. “The Multi-Cover Persistence of Euclidean Balls,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.34\">https://doi.org/10.4230/LIPIcs.SoCG.2018.34</a>.","ista":"Edelsbrunner H, Osang GF. 2018. The multi-cover persistence of Euclidean balls. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 34."},"author":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert"},{"first_name":"Georg F","last_name":"Osang","orcid":"0000-0002-8882-5116","full_name":"Osang, Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2018","title":"The multi-cover persistence of Euclidean balls","_id":"187","ddc":["516"],"oa":1,"related_material":{"record":[{"status":"public","relation":"later_version","id":"9317"},{"status":"public","relation":"dissertation_contains","id":"9056"}]},"project":[{"name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"abstract":[{"lang":"eng","text":"Given a locally finite X ⊆ ℝd and a radius r ≥ 0, the k-fold cover of X and r consists of all points in ℝd that have k or more points of X within distance r. We consider two filtrations - one in scale obtained by fixing k and increasing r, and the other in depth obtained by fixing r and decreasing k - and we compute the persistence diagrams of both. While standard methods suffice for the filtration in scale, we need novel geometric and topological concepts for the filtration in depth. In particular, we introduce a rhomboid tiling in ℝd+1 whose horizontal integer slices are the order-k Delaunay mosaics of X, and construct a zigzag module from Delaunay mosaics that is isomorphic to the persistence module of the multi-covers. "}],"publication_status":"published"},{"day":"11","oa_version":"Published Version","type":"conference","date_updated":"2021-01-12T06:53:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This research is partially supported by the Office of Naval Research, through grant no. N62909-18-1-2038, and the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund","has_accepted_license":"1","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.SoCG.2018.35","page":"35:1 - 35:13","file":[{"date_created":"2018-12-17T16:31:31Z","relation":"main_file","content_type":"application/pdf","creator":"dernst","file_size":489080,"date_updated":"2020-07-14T12:45:20Z","file_id":"5724","access_level":"open_access","checksum":"7509403803b3ac1aee94bbc2ad293d21","file_name":"2018_LIPIcs_Edelsbrunner.pdf"}],"date_published":"2018-06-11T00:00:00Z","scopus_import":1,"alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"year":"2018","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"first_name":"Ziga","last_name":"Virk","full_name":"Virk, Ziga"},{"id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Hubert","first_name":"Hubert","last_name":"Wagner"}],"quality_controlled":"1","citation":{"short":"H. Edelsbrunner, Z. Virk, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13.","chicago":"Edelsbrunner, Herbert, Ziga Virk, and Hubert Wagner. “Smallest Enclosing Spheres and Chernoff Points in Bregman Geometry,” 99:35:1-35:13. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.35\">https://doi.org/10.4230/LIPIcs.SoCG.2018.35</a>.","ista":"Edelsbrunner H, Virk Z, Wagner H. 2018. Smallest enclosing spheres and Chernoff points in Bregman geometry. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 35:1-35:13.","ieee":"H. Edelsbrunner, Z. Virk, and H. Wagner, “Smallest enclosing spheres and Chernoff points in Bregman geometry,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 35:1-35:13.","ama":"Edelsbrunner H, Virk Z, Wagner H. Smallest enclosing spheres and Chernoff points in Bregman geometry. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:35:1-35:13. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.35\">10.4230/LIPIcs.SoCG.2018.35</a>","apa":"Edelsbrunner, H., Virk, Z., &#38; Wagner, H. (2018). Smallest enclosing spheres and Chernoff points in Bregman geometry (Vol. 99, p. 35:1-35:13). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.35\">https://doi.org/10.4230/LIPIcs.SoCG.2018.35</a>","mla":"Edelsbrunner, Herbert, et al. <i>Smallest Enclosing Spheres and Chernoff Points in Bregman Geometry</i>. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.35\">10.4230/LIPIcs.SoCG.2018.35</a>."},"abstract":[{"text":"Smallest enclosing spheres of finite point sets are central to methods in topological data analysis. Focusing on Bregman divergences to measure dissimilarity, we prove bounds on the location of the center of a smallest enclosing sphere. These bounds depend on the range of radii for which Bregman balls are convex.","lang":"eng"}],"publication_status":"published","project":[{"name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"_id":"188","ddc":["000"],"oa":1,"title":"Smallest enclosing spheres and Chernoff points in Bregman geometry","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file_date_updated":"2020-07-14T12:45:20Z","volume":99,"status":"public","month":"06","conference":{"name":"SoCG: Symposium on Computational Geometry","end_date":"2018-06-14","start_date":"2018-06-11","location":"Budapest, Hungary"},"date_created":"2018-12-11T11:45:05Z","publist_id":"7733","intvolume":"        99"},{"issue":"11","volume":35,"article_type":"original","publisher":"Oxford University Press","intvolume":"        35","publist_id":"8036","isi":1,"date_created":"2018-12-11T11:44:11Z","month":"08","status":"public","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30169679","open_access":"1"}],"citation":{"apa":"Palmer, A., Chait, R. P., &#38; Kishony, R. (2018). Nonoptimal gene expression creates latent potential for antibiotic resistance. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msy163\">https://doi.org/10.1093/molbev/msy163</a>","mla":"Palmer, Adam, et al. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” <i>Molecular Biology and Evolution</i>, vol. 35, no. 11, Oxford University Press, 2018, pp. 2669–84, doi:<a href=\"https://doi.org/10.1093/molbev/msy163\">10.1093/molbev/msy163</a>.","ieee":"A. Palmer, R. P. Chait, and R. Kishony, “Nonoptimal gene expression creates latent potential for antibiotic resistance,” <i>Molecular Biology and Evolution</i>, vol. 35, no. 11. Oxford University Press, pp. 2669–2684, 2018.","ama":"Palmer A, Chait RP, Kishony R. Nonoptimal gene expression creates latent potential for antibiotic resistance. <i>Molecular Biology and Evolution</i>. 2018;35(11):2669-2684. doi:<a href=\"https://doi.org/10.1093/molbev/msy163\">10.1093/molbev/msy163</a>","ista":"Palmer A, Chait RP, Kishony R. 2018. Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. 35(11), 2669–2684.","short":"A. Palmer, R.P. Chait, R. Kishony, Molecular Biology and Evolution 35 (2018) 2669–2684.","chicago":"Palmer, Adam, Remy P Chait, and Roy Kishony. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/molbev/msy163\">https://doi.org/10.1093/molbev/msy163</a>."},"author":[{"first_name":"Adam","last_name":"Palmer","full_name":"Palmer, Adam"},{"first_name":"Remy P","last_name":"Chait","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","full_name":"Chait, Remy P","orcid":"0000-0003-0876-3187"},{"full_name":"Kishony, Roy","first_name":"Roy","last_name":"Kishony"}],"quality_controlled":"1","year":"2018","publication":"Molecular Biology and Evolution","title":"Nonoptimal gene expression creates latent potential for antibiotic resistance","pmid":1,"oa":1,"_id":"19","publication_status":"published","abstract":[{"lang":"eng","text":"Bacteria regulate genes to survive antibiotic stress, but regulation can be far from perfect. When regulation is not optimal, mutations that change gene expression can contribute to antibiotic resistance. It is not systematically understood to what extent natural gene regulation is or is not optimal for distinct antibiotics, and how changes in expression of specific genes quantitatively affect antibiotic resistance. Here we discover a simple quantitative relation between fitness, gene expression, and antibiotic potency, which rationalizes our observation that a multitude of genes and even innate antibiotic defense mechanisms have expression that is critically nonoptimal under antibiotic treatment. First, we developed a pooled-strain drug-diffusion assay and screened Escherichia coli overexpression and knockout libraries, finding that resistance to a range of 31 antibiotics could result from changing expression of a large and functionally diverse set of genes, in a primarily but not exclusively drug-specific manner. Second, by synthetically controlling the expression of single-drug and multidrug resistance genes, we observed that their fitness-expression functions changed dramatically under antibiotic treatment in accordance with a log-sensitivity relation. Thus, because many genes are nonoptimally expressed under antibiotic treatment, many regulatory mutations can contribute to resistance by altering expression and by activating latent defenses."}],"date_published":"2018-08-28T00:00:00Z","external_id":{"isi":["000452567200006"],"pmid":["30169679"]},"page":"2669 - 2684","publication_identifier":{"issn":["0737-4038"]},"scopus_import":"1","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","date_updated":"2023-10-17T11:51:06Z","oa_version":"Submitted Version","day":"28","doi":"10.1093/molbev/msy163","language":[{"iso":"eng"}],"department":[{"_id":"CaGu"},{"_id":"GaTk"}]},{"scopus_import":"1","page":"254-264","external_id":{"isi":["000443231000002"],"pmid":["29998472"]},"date_published":"2018-07-11T00:00:00Z","department":[{"_id":"BeVi"}],"doi":"10.1002/jez.b.22824","language":[{"iso":"eng"}],"day":"11","oa_version":"Submitted Version","date_updated":"2023-09-11T13:59:54Z","type":"journal_article","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","month":"07","date_created":"2018-12-11T11:45:06Z","isi":1,"publist_id":"7730","intvolume":"       330","publisher":"Wiley","article_type":"original","volume":330,"abstract":[{"lang":"eng","text":"The German cockroach, Blattella germanica, is a worldwide pest that infests buildings, including homes, restaurants, and hospitals, often living in unsanitary conditions. As a disease vector and producer of allergens, this species has major health and economic impacts on humans. Factors contributing to the success of the German cockroach include its resistance to a broad range of insecticides, immunity to many pathogens, and its ability, as an extreme generalist omnivore, to survive on most food sources. The recently published genome shows that B. germanica has an exceptionally high number of protein coding genes. In this study, we investigate the functions of the 93 significantly expanded gene families with the aim to better understand the success of B. germanica as a major pest despite such inhospitable conditions. We find major expansions in gene families with functions related to the detoxification of insecticides and allelochemicals, defense against pathogens, digestion, sensory perception, and gene regulation. These expansions might have allowed B. germanica to develop multiple resistance mechanisms to insecticides and pathogens, and enabled a broad, flexible diet, thus explaining its success in unsanitary conditions and under recurrent chemical control. The findings and resources presented here provide insights for better understanding molecular mechanisms that will facilitate more effective cockroach control."}],"publication_status":"published","_id":"190","oa":1,"pmid":1,"publication":"Journal of Experimental Zoology Part B: Molecular and Developmental Evolution","title":"Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest","year":"2018","author":[{"full_name":"Harrison, Mark","first_name":"Mark","last_name":"Harrison"},{"full_name":"Arning, Nicolas","first_name":"Nicolas","last_name":"Arning"},{"full_name":"Kremer, Lucas","last_name":"Kremer","first_name":"Lucas"},{"first_name":"Guillem","last_name":"Ylla","full_name":"Ylla, Guillem"},{"last_name":"Belles","first_name":"Xavier","full_name":"Belles, Xavier"},{"full_name":"Bornberg Bauer, Erich","last_name":"Bornberg Bauer","first_name":"Erich"},{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8871-4961","full_name":"Huylmans, Ann K","first_name":"Ann K","last_name":"Huylmans"},{"first_name":"Evelien","last_name":"Jongepier","full_name":"Jongepier, Evelien"},{"last_name":"Puilachs","first_name":"Maria","full_name":"Puilachs, Maria"},{"first_name":"Stephen","last_name":"Richards","full_name":"Richards, Stephen"},{"full_name":"Schal, Coby","first_name":"Coby","last_name":"Schal"}],"quality_controlled":"1","citation":{"mla":"Harrison, Mark, et al. “Expansions of Key Protein Families in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>, vol. 330, Wiley, 2018, pp. 254–64, doi:<a href=\"https://doi.org/10.1002/jez.b.22824\">10.1002/jez.b.22824</a>.","apa":"Harrison, M., Arning, N., Kremer, L., Ylla, G., Belles, X., Bornberg Bauer, E., … Schal, C. (2018). Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. Wiley. <a href=\"https://doi.org/10.1002/jez.b.22824\">https://doi.org/10.1002/jez.b.22824</a>","short":"M. Harrison, N. Arning, L. Kremer, G. Ylla, X. Belles, E. Bornberg Bauer, A.K. Huylmans, E. Jongepier, M. Puilachs, S. Richards, C. Schal, Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 330 (2018) 254–264.","chicago":"Harrison, Mark, Nicolas Arning, Lucas Kremer, Guillem Ylla, Xavier Belles, Erich Bornberg Bauer, Ann K Huylmans, et al. “Expansions of Key Protein Families in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/jez.b.22824\">https://doi.org/10.1002/jez.b.22824</a>.","ista":"Harrison M, Arning N, Kremer L, Ylla G, Belles X, Bornberg Bauer E, Huylmans AK, Jongepier E, Puilachs M, Richards S, Schal C. 2018. Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 330, 254–264.","ama":"Harrison M, Arning N, Kremer L, et al. Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. 2018;330:254-264. doi:<a href=\"https://doi.org/10.1002/jez.b.22824\">10.1002/jez.b.22824</a>","ieee":"M. Harrison <i>et al.</i>, “Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest,” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>, vol. 330. Wiley, pp. 254–264, 2018."},"main_file_link":[{"url":"https://onlinelibrary.wiley.com/doi/am-pdf/10.1002/jez.b.22824","open_access":"1"}]},{"ec_funded":1,"department":[{"_id":"JiFr"},{"_id":"EvBe"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"doi":"10.1038/s41598-018-28188-1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","oa_version":"Published Version","date_updated":"2025-05-07T11:12:31Z","type":"journal_article","day":"06","scopus_import":"1","file":[{"checksum":"266b03f4fb8198e83141617aaa99dcab","file_name":"2018_ScientificReports_Grones.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:20Z","file_id":"5714","creator":"dernst","content_type":"application/pdf","file_size":2413876,"relation":"main_file","date_created":"2018-12-17T15:38:56Z"}],"external_id":{"isi":["000437673200053"]},"date_published":"2018-07-06T00:00:00Z","title":"PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism","publication":"Scientific Reports","_id":"191","ddc":["581"],"oa":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8822"}]},"project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"}],"abstract":[{"lang":"eng","text":"Intercellular distribution of the plant hormone auxin largely depends on the polar subcellular distribution of the plasma membrane PIN-FORMED (PIN) auxin transporters. PIN polarity switches in response to different developmental and environmental signals have been shown to redirect auxin fluxes mediating certain developmental responses. PIN phosphorylation at different sites and by different kinases is crucial for PIN function. Here we investigate the role of PIN phosphorylation during gravitropic response. Loss- and gain-of-function mutants in PINOID and related kinases but not in D6PK kinase as well as mutations mimicking constitutive dephosphorylated or phosphorylated status of two clusters of predicted phosphorylation sites partially disrupted PIN3 phosphorylation and caused defects in gravitropic bending in roots and hypocotyls. In particular, they impacted PIN3 polarity rearrangements in response to gravity and during feed-back regulation by auxin itself. Thus PIN phosphorylation, besides regulating transport activity and apical-basal targeting, is also important for the rapid polarity switches in response to environmental and endogenous signals."}],"publication_status":"published","citation":{"apa":"Grones, P., Abas, M. F., Hajny, J., Jones, A., Waidmann, S., Kleine Vehn, J., &#38; Friml, J. (2018). PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. <i>Scientific Reports</i>. Springer. <a href=\"https://doi.org/10.1038/s41598-018-28188-1\">https://doi.org/10.1038/s41598-018-28188-1</a>","mla":"Grones, Peter, et al. “PID/WAG-Mediated Phosphorylation of the Arabidopsis PIN3 Auxin Transporter Mediates Polarity Switches during Gravitropism.” <i>Scientific Reports</i>, vol. 8, no. 1, 10279, Springer, 2018, doi:<a href=\"https://doi.org/10.1038/s41598-018-28188-1\">10.1038/s41598-018-28188-1</a>.","ieee":"P. Grones <i>et al.</i>, “PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism,” <i>Scientific Reports</i>, vol. 8, no. 1. Springer, 2018.","ama":"Grones P, Abas MF, Hajny J, et al. PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. <i>Scientific Reports</i>. 2018;8(1). doi:<a href=\"https://doi.org/10.1038/s41598-018-28188-1\">10.1038/s41598-018-28188-1</a>","chicago":"Grones, Peter, Melinda F Abas, Jakub Hajny, Angharad Jones, Sascha Waidmann, Jürgen Kleine Vehn, and Jiří Friml. “PID/WAG-Mediated Phosphorylation of the Arabidopsis PIN3 Auxin Transporter Mediates Polarity Switches during Gravitropism.” <i>Scientific Reports</i>. Springer, 2018. <a href=\"https://doi.org/10.1038/s41598-018-28188-1\">https://doi.org/10.1038/s41598-018-28188-1</a>.","short":"P. Grones, M.F. Abas, J. Hajny, A. Jones, S. Waidmann, J. Kleine Vehn, J. Friml, Scientific Reports 8 (2018).","ista":"Grones P, Abas MF, Hajny J, Jones A, Waidmann S, Kleine Vehn J, Friml J. 2018. PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. Scientific Reports. 8(1), 10279."},"quality_controlled":"1","author":[{"id":"399876EC-F248-11E8-B48F-1D18A9856A87","full_name":"Grones, Peter","first_name":"Peter","last_name":"Grones"},{"first_name":"Melinda F","last_name":"Abas","id":"3CFB3B1C-F248-11E8-B48F-1D18A9856A87","full_name":"Abas, Melinda F"},{"id":"4800CC20-F248-11E8-B48F-1D18A9856A87","full_name":"Hajny, Jakub","orcid":"0000-0003-2140-7195","first_name":"Jakub","last_name":"Hajny"},{"full_name":"Jones, Angharad","last_name":"Jones","first_name":"Angharad"},{"full_name":"Waidmann, Sascha","first_name":"Sascha","last_name":"Waidmann"},{"full_name":"Kleine Vehn, Jürgen","last_name":"Kleine Vehn","first_name":"Jürgen"},{"last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2018","intvolume":"         8","isi":1,"publist_id":"7729","month":"07","date_created":"2018-12-11T11:45:06Z","article_number":"10279","status":"public","volume":8,"issue":"1","file_date_updated":"2020-07-14T12:45:20Z","publisher":"Springer"},{"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"25","type":"journal_article","date_updated":"2023-09-15T12:11:03Z","oa_version":"Submitted Version","doi":"10.1038/s41477-018-0190-1","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"},{"_id":"DaSi"},{"_id":"NanoFab"}],"page":"453 - 459","date_published":"2018-06-25T00:00:00Z","external_id":{"isi":["000443221200017"],"pmid":["29942048"]},"scopus_import":"1","quality_controlled":"1","author":[{"id":"43905548-F248-11E8-B48F-1D18A9856A87","full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","last_name":"Fendrych","first_name":"Matyas"},{"id":"3425EC26-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1522-3162","full_name":"Akhmanova, Maria","first_name":"Maria","last_name":"Akhmanova"},{"first_name":"Jack","last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Glanc, Matous","last_name":"Glanc","first_name":"Matous"},{"full_name":"Hagihara, Shinya","last_name":"Hagihara","first_name":"Shinya"},{"full_name":"Takahashi, Koji","first_name":"Koji","last_name":"Takahashi"},{"first_name":"Naoyuki","last_name":"Uchida","full_name":"Uchida, Naoyuki"},{"full_name":"Torii, Keiko U","last_name":"Torii","first_name":"Keiko U"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29942048"}],"citation":{"apa":"Fendrych, M., Akhmanova, M., Merrin, J., Glanc, M., Hagihara, S., Takahashi, K., … Friml, J. (2018). Rapid and reversible root growth inhibition by TIR1 auxin signalling. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-018-0190-1\">https://doi.org/10.1038/s41477-018-0190-1</a>","mla":"Fendrych, Matyas, et al. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” <i>Nature Plants</i>, vol. 4, no. 7, Springer Nature, 2018, pp. 453–59, doi:<a href=\"https://doi.org/10.1038/s41477-018-0190-1\">10.1038/s41477-018-0190-1</a>.","ista":"Fendrych M, Akhmanova M, Merrin J, Glanc M, Hagihara S, Takahashi K, Uchida N, Torii KU, Friml J. 2018. Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. 4(7), 453–459.","chicago":"Fendrych, Matyas, Maria Akhmanova, Jack Merrin, Matous Glanc, Shinya Hagihara, Koji Takahashi, Naoyuki Uchida, Keiko U Torii, and Jiří Friml. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” <i>Nature Plants</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41477-018-0190-1\">https://doi.org/10.1038/s41477-018-0190-1</a>.","short":"M. Fendrych, M. Akhmanova, J. Merrin, M. Glanc, S. Hagihara, K. Takahashi, N. Uchida, K.U. Torii, J. Friml, Nature Plants 4 (2018) 453–459.","ama":"Fendrych M, Akhmanova M, Merrin J, et al. Rapid and reversible root growth inhibition by TIR1 auxin signalling. <i>Nature Plants</i>. 2018;4(7):453-459. doi:<a href=\"https://doi.org/10.1038/s41477-018-0190-1\">10.1038/s41477-018-0190-1</a>","ieee":"M. Fendrych <i>et al.</i>, “Rapid and reversible root growth inhibition by TIR1 auxin signalling,” <i>Nature Plants</i>, vol. 4, no. 7. Springer Nature, pp. 453–459, 2018."},"year":"2018","oa":1,"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/new-mechanism-for-the-plant-hormone-auxin-discovered/"}]},"_id":"192","title":"Rapid and reversible root growth inhibition by TIR1 auxin signalling","publication":"Nature Plants","pmid":1,"publication_status":"published","abstract":[{"text":"The phytohormone auxin is the information carrier in a plethora of developmental and physiological processes in plants(1). It has been firmly established that canonical, nuclear auxin signalling acts through regulation of gene transcription(2). Here, we combined microfluidics, live imaging, genetic engineering and computational modelling to reanalyse the classical case of root growth inhibition(3) by auxin. We show that Arabidopsis roots react to addition and removal of auxin by extremely rapid adaptation of growth rate. This process requires intracellular auxin perception but not transcriptional reprogramming. The formation of the canonical TIR1/AFB-Aux/IAA co-receptor complex is required for the growth regulation, hinting to a novel, non-transcriptional branch of this signalling pathway. Our results challenge the current understanding of root growth regulation by auxin and suggest another, presumably non-transcriptional, signalling output of the canonical auxin pathway.","lang":"eng"}],"issue":"7","volume":4,"article_type":"original","publisher":"Springer Nature","publist_id":"7728","isi":1,"intvolume":"         4","status":"public","date_created":"2018-12-11T11:45:07Z","month":"06"}]